My, my, you certainly are making some serious conspiratorial accusations there. Do you have any evidence to support these allegations? Again, I'm well aware that there can be (and are) abuses. However, if such is going to be claimed, evidence needs to be presented. Even then, it does not follow from the description "big and cost inefficient" that an organization is conspiring to get tax breaks. Heck, it seems more logical to me to note that non-profits typically offer low salaries and therefore can't recruit the best people for the job (thus mistakes happen more often). Serious accusations demand serious evidence.
Regardless, as someone who has little to no background in finance and operations of organizations, I'm not in a position to evaluate such evidence properly even if it were presented. This means if I whine about "mismanagement" of certain religious organization's finances I'd be doing little more than making ill-informed judgements grounded in mere prejudice instead of reason. I have little comment other than to suggest one not oversimplify the picture and question whether the abuses of a few justify spoiling the entire pot.